8QKT

Structure of a nucleosome composed of a palindromic 167-base pair blunt-ended DNA fragment


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 3UT9 

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP291MnCl2-containing buffers
Crystal Properties
Matthews coefficientSolvent content
2.7655.47

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 108.437α = 90
b = 103.722β = 93.59
c = 185.405γ = 90
Symmetry
Space GroupP 1 21 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100PIXELDECTRIS PILATUS 2M-F2014-10-10MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONSLS BEAMLINE X06DA0.9SLSX06DA

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)CC (Half)Net I Over Average Sigma (I)RedundancyNumber Reflections (All)Number Reflections (Observed)Observed Criterion Sigma (F)Observed Criterion Sigma (I)B (Isotropic) From Wilson Plot
13.2648.66960.9978.93.261655
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)CC (Half)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
13.263.440.541

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodResolution (High)Resolution (Low)Number Reflections (Observed)Number Reflections (R-Free)Percent Reflections (Observed)R-Factor (All)R-WorkR-FreeMean Isotropic B
X-RAY DIFFRACTIONMOLECULAR REPLACEMENTFREE R-VALUE3.26148.65557291286589.0610.2720.26920.32188.517
Temperature Factor Modeling
Anisotropic B[1][1]Anisotropic B[1][2]Anisotropic B[1][3]Anisotropic B[2][2]Anisotropic B[2][3]Anisotropic B[3][3]
-2.504-0.466-1.8184.346
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg28.49
r_dihedral_angle_3_deg16.373
r_dihedral_angle_4_deg15.954
r_lrange_it7.703
r_lrange_other7.703
r_dihedral_angle_1_deg5.064
r_scangle_it4.717
r_scangle_other4.716
r_mcangle_it4.115
r_mcangle_other4.115
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg28.49
r_dihedral_angle_3_deg16.373
r_dihedral_angle_4_deg15.954
r_lrange_it7.703
r_lrange_other7.703
r_dihedral_angle_1_deg5.064
r_scangle_it4.717
r_scangle_other4.716
r_mcangle_it4.115
r_mcangle_other4.115
r_scbond_it2.758
r_scbond_other2.758
r_mcbond_it2.351
r_mcbond_other2.351
r_angle_other_deg2.296
r_angle_refined_deg1.232
r_symmetry_nbd_refined0.264
r_nbd_other0.249
r_symmetry_nbd_other0.222
r_nbtor_refined0.211
r_nbd_refined0.178
r_symmetry_xyhbond_nbd_refined0.165
r_xyhbond_nbd_refined0.128
r_chiral_restr0.093
r_symmetry_nbtor_other0.075
r_symmetry_xyhbond_nbd_other0.045
r_bond_other_d0.027
r_bond_refined_d0.009
r_gen_planes_refined0.003
r_gen_planes_other0.003
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms11980
Nucleic Acid Atoms13682
Solvent Atoms
Heterogen Atoms33

Software

Software
Software NamePurpose
REFMACrefinement
XDSdata reduction
SCALAdata scaling
MOLREPphasing